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Lukas Valihrach, PhD


Lukáš Valihrach, PhD

Senior Scientist

Publons, GoogleScholar, Twitter


Areas of expertise

  • Single-cell transcriptomics
  • Spatial transcriptomics
  • Data analysis
  • Neurobiology
  • Glial cell
  • Method development
  • microRNA


I am a senior researcher in Laboratory of Gene Expression at Institute of Biotechnology of the Czech Academy of Sciences. I received PhD at University of Chemistry and Technology in Prague, Czech Republic and I worked as an intern in Denmark and Sweden. My long-term interest is analysis of single-cell gene expression using RNA sequencing and RT-qPCR. I am also active in method development and implementation (see our Two-tailed technology for analysis of short RNAs). My primary research focus is on glial cells and their role under pathophysiological conditions. I am involved in the projects focused on the analysis of experimental ischemic stroke and spinal cord injury, amyotrophic lateral sclerosis or Alexander disease. In addition to research, I enjoy training young students and learning new things. When not in lab, I love spending time with my wife, daughters and overactive dog, running in the mountains and occasionally partying with friends;)



  • GA23-05327S     Astrocyte-microglia communication as a target for stroke therapy. 2023-2025.
  • GA23-06269S     Disturbed regulation of mTOR signaling in glial cells following cerebral ischemia. 2023-2025.
  • GA22-10660S     The role of Meis transcription factors in mesenchymal condensations during formation of the cranium. 2022-2024.
  • NU21-08-00286  Circulating microRNAs as biomarkers for evaluating the severity of acute spinal cord injury. 2021-2024.
  • EJPRD19-256     ALEXANDER - The astrocyte nanofilament system in Alexander disease – from molecules to function, uncovering new leads for therapy. 2020-2022.
  • GA20-05770S     The role of glial TRPV4 channels in brain edema formation and post-ischemic regeneration. 2020-2022.
  • GA19-02046S     Glial cells- the key players in the progression of amyotrophic lateral sclerosis. 2019-2021.
  • GA18-21942S     MicroRNA in central nervous system injury: potential roles and therapeutic implications. 2018-2020.
  • GA17-04034S     Principal signaling pathways regulating NG2 glia proliferation and differentiation following brain injuries. 2017-2019.
  • GA16-10214S     Age-related changes in brain diffusivity, extracellular matrix composition and glial physiology - impact on pathogenesis of ischemia. 2016-2018.
  • GA13-02154S     Gene expression profiling and functional characterization of glial cell subpopulations following ischemic brain injury. 2013-2016.


Technology Development

Editorial Board Membership

Selected Publications

  1. Spatiotemporal transcriptomic map of ischemic brain injury. Zucha D, Abaffy P, Kirdajova D, Jirak D, Anderova M, Kubista M, Valihrach L. BioRxiv 2023.03.28.534553; doi: 10.1101/2023.03.28.534553.
  2. NEUROD1 reinforces endocrine cell fate acquisition in pancreatic development. Bohuslavova R, Fabriciova V, Smolik O, Lebrón-Mora L, Abaffy P, Benesova S, Zucha D, Valihrach L, Berkova Z, Saudek F, Pavlinkova G. Nat Commun. 2023 Sep 9;14(1):5554. doi: 10.1038/s41467-023-41306-6. IF = 16.6.
  3. Complement C3a treatment accelerates recovery after stroke via modulation of astrocyte reactivity and cortical connectivity. Stokowska A, Aswendt M, Zucha D, Lohmann S, Wieters F, Moran Suarez J, Atkins AL, Li Y, Miteva M, Lewin J, Wiedermann D, Diedenhofen M, Torinsson Naluai Å, Abaffy P, Valihrach L, Kubista M, Hoehn M, Pekny M, Pekna M. J Clin Invest. 2023 Mar 30:e162253. doi: 10.1172/JCI162253. IF = 19.456.
  4. ISL1 is necessary for auditory neuron development and contributes toward tonotopic organization. Filova I, Pysanenko K, Tavakoli M, Vochyanova S, Dvorakova M, Bohuslavova R, Smolik O, Fabriciova V, Hrabalova P, Benesova S, Valihrach L, Cerny J, Yamoah EN, Syka J, Fritzsch B, Pavlinkova G. Proc Natl Acad Sci U S A. 2022 Sep 13;119(37):e2207433119. doi: 10.1073/pnas.2207433119. IF = 12.779.
  5. Small RNA-Sequencing for Analysis of Circulating miRNAs: Benchmark Study. Androvic P, Benesova S, Rohlova E, Kubista M, Valihrach L. J Mol Diagn. 2022 Jan 23:S1525-1578(22)00011-3. doi: 10.1016/j.jmoldx.2021.12.006. IF = 5.568.
  6. Transient astrocyte-like NG2 glia subpopulation emerges solely following permanent brain ischemia. Kirdajova D, Valihrach L, Valny M, Kriska J, Krocianova D, Benesova S, Abaffy P, Zucha D, Klassen R, Kolenicova D, Honsa P, Kubista M, Anderova M. Glia. 2021 Jul 27. doi: 10.1002/glia.24064. IF = 8.073.
  7. Decoding the transcriptional response to ischemic stroke in young and aged mouse brain. Androvic P, Belov Kirdajova D, Tureckova J, Zucha D, Rohlova E, Abaffy P, Kriska J, Anderova M, Kubista M, Valihrach L. Cell Rep. 2020 Jun 16;31(11):107777. doi: 10.1016/j.celrep.2020.107777. IF = 9.423.
  8. Performance Comparison of Reverse Transcriptases for Single-Cell Studies. Zucha D, Androvic P, Kubista M, Valihrach L. Clin Chem. 2019 Nov 7. pii: clinchem.2019.307835. doi: 10.1373/clinchem.2019.307835. IF = 8.327.
  9. Circulating miRNA analysis for cancer diagnostics and therapy. Valihrach L, Androvic P, Kubista M. Mol Aspects Med. 2019 Oct 18:100825. doi: 10.1016/j.mam.2019.10.002. IF = 14.235.
  10. Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification. Androvic P, Valihrach L, Elling J, Sjoback R, Kubista M. Nucleic Acids Res. 2017 Sep 6;45(15):e144. doi: 10.1093/nar/gkx588. IF = 11.147.

Invited Lectures